Openeye python libraries - Revision history

Khtang: /* OpenEye Python 3 Toolkit 2018 */

2019-03-13T23:32:27Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 23:32, 13 March 2019
Line 27:		Line 27:
	====Here is how to install with Conda environment====		====Here is how to install with Conda environment====

	Download '''Conda3''' installer file to directory that you would like to install (Please check /nfs/soft if there is on already installed)		Download '''Conda3''' installer file to directory that you would like to install (Please check /nfs/soft if there is one already installed)
	wget https://repo.anaconda.com/archive/Anaconda3-2018.12-Linux-x86_64.sh		wget https://repo.anaconda.com/archive/Anaconda3-2018.12-Linux-x86_64.sh
	bash Anaconda3-2018.12-Linux-x86_64.sh		bash Anaconda3-2018.12-Linux-x86_64.sh

Khtang: /* OpenEye Python 3 Toolkit 2018 */

2019-03-13T23:22:28Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 23:22, 13 March 2019
Line 17:		Line 17:
	===OpenEye Python 3 Toolkit 2018===		===OpenEye Python 3 Toolkit 2018===
	Due to the nature of nfs-soft being a CentOS 6 server, we must run the most current version of OpenEye through a conda/miniconda with Python3 environment. <br />		Due to the nature of nfs-soft being a CentOS 6 server, we must run the most current version of OpenEye through a conda/miniconda with Python3 environment. <br />
	See page on conda: http://wiki.docking.org/index.php/Install_Miniconda <br />		See page on conda: http://wiki.docking.org/index.php/Install_Miniconda <br />
			Here is the [https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html#installing-openeye-python-toolkits page on OpenEye website] explaining different ways to set it up.

	If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error		If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error

	ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found		ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
	(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)		(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)

			====Here is how to install with Conda environment====

			Download '''Conda3''' installer file to directory that you would like to install (Please check /nfs/soft if there is on already installed)
			wget https://repo.anaconda.com/archive/Anaconda3-2018.12-Linux-x86_64.sh
			bash Anaconda3-2018.12-Linux-x86_64.sh
			# pre-end /path/to/install/tools/anaconda3 for install path and let installer finish

			After Conda3 is installed, create conda environment for OpenEye Python Toolkit

			conda create -n oepython3 python=3

	Activate compatible conda python environment		Activate compatible conda python environment

Benrwong: /* OpenEye Python 3 Toolkit 2018 */

2018-10-17T00:22:22Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 00:22, 17 October 2018
Line 16:		Line 16:

	===OpenEye Python 3 Toolkit 2018===		===OpenEye Python 3 Toolkit 2018===
	Due to the nature of nfs-soft being a ~~CentOS6~~ server, we must run the most current version of OpenEye through a conda/miniconda with Python3 environment. <br />		Due to the nature of nfs-soft being a CentOS 6 server, we must run the most current version of OpenEye through a conda/miniconda with Python3 environment. <br />
	See page on conda: http://wiki.docking.org/index.php/Install_Miniconda <br />		See page on conda: http://wiki.docking.org/index.php/Install_Miniconda <br />
	If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error		If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error
Line 37:		Line 37:
	Downgrade to pip 9.0.3 to avoid it.		Downgrade to pip 9.0.3 to avoid it.
	$ '''pip install --upgrade pip==9.0.3'''		$ '''pip install --upgrade pip==9.0.3'''

			Run OpenEye tests to see if configuration works:
			(oepython3) $ '''python /mnt/nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/examples/openeye_tests.py'''
			(oepython3) $ '''python /mnt/nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/examples/oechem/oecheminfo.py'''
			Installed OEChem version: 2.1.4 platform: linux-g++4.x-x64 built: 20180215


	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Benrwong: /* OpenEye Python 3 Toolkit 2018 */

2018-10-17T00:05:49Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 00:05, 17 October 2018
Line 28:		Line 28:
	source relevant openeye environment and license		source relevant openeye environment and license
	(oepython3) $ '''source /mnt/nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/env.sh'''		(oepython3) $ '''source /mnt/nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/env.sh'''


			Running some commands may run into below error. This is a pip issue with pip version >10.
			AttributeError: module 'pip' has no attribute 'main'
			(oepython3) $ pip -V
			pip 10.0.1 from /home/s_bwong1/miniconda3/envs/oepython3/lib/python3.7/site-packages/pip (python 3.7)

			Downgrade to pip 9.0.3 to avoid it.
			$ '''pip install --upgrade pip==9.0.3'''


	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Benrwong: /* OpenEye Python 3 Toolkit 2018 */

2018-10-16T22:28:03Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 22:28, 16 October 2018
Line 23:		Line 23:
	(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)		(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)

	Activate compatible python environment		Activate compatible conda python environment
	$ '''source activate oepython3'''		$ '''source activate oepython3'''

Benrwong: /* OpenEye Python 3 Toolkit 2018 */

2018-10-16T22:23:47Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 22:23, 16 October 2018
Line 23:		Line 23:
	(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)		(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)

			Activate compatible python environment
			$ '''source activate oepython3'''

			source relevant openeye environment and license
			(oepython3) $ '''source /mnt/nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/env.sh'''

	[[Category:Internal]]		[[Category:Internal]]
			[[Category:Sysadmin]]

Benrwong: /* OpenEye Python 3 Toolkit 2018 */

2018-10-16T22:19:53Z

OpenEye Python 3 Toolkit 2018

← Older revision		Revision as of 22:19, 16 October 2018
Line 16:		Line 16:

	===OpenEye Python 3 Toolkit 2018===		===OpenEye Python 3 Toolkit 2018===
	Due to the nature of nfs-soft being a CentOS6 server, we must run the most current version of OpenEye through a conda/miniconda environment.		Due to the nature of nfs-soft being a CentOS6 server, we must run the most current version of OpenEye through a conda/miniconda with Python3 environment. <br />
			See page on conda: http://wiki.docking.org/index.php/Install_Miniconda <br />
	If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error		If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error

Benrwong: openeye 2018

2018-10-16T21:50:45Z

openeye 2018

← Older revision		Revision as of 21:50, 16 October 2018
Line 14:		Line 14:

	Alternatively you can use the /nfs/soft/python/envs/complete/latest environment. It has openeye installed.		Alternatively you can use the /nfs/soft/python/envs/complete/latest environment. It has openeye installed.

			===OpenEye Python 3 Toolkit 2018===
			Due to the nature of nfs-soft being a CentOS6 server, we must run the most current version of OpenEye through a conda/miniconda environment.
			If you run openeye from nfs-soft without a conda environment, you will run into an issue with a /usr/lib64/libstdc++.so.6 error

			ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
			(required by /nfs/soft/openeye/OpenEye-toolkits-python3-linux-x64-2018.2.1/openeye/libs/python3-linux-x64-g++4.x/liboebio-2.1.4.so)




	[[Category:Internal]]		[[Category:Internal]]

Frodo: asdf

2015-05-21T01:41:41Z

asdf

New page

They provide a "nice" python package that can be installed in a virtualenv.

I've copied the contents of this to /nfs/soft/openeye/current/python to emulate the Cluster 0 behavior.

However the "best" approach may be to create a virtualenv and install it in there.
That way you're isolated from any changes that may happened on the cluster versions: This should do it all:

/nfs/soft/python/install/scripts/create-virtualenv.sh /nfs/soft/python/envs/vanilla/python-2.7.7 ~/my-python-env
# Wait a bit
/nfs/soft/python/envs/vanilla/python-2.7.7/bin/pip freeze > ~/my-python-env/requirements.txt
source ~/my-python-env/bin/activate.[c]sh
pip install -r ~/my-python-env/requirements.txt
pip install /nfs/soft/openeye/install/centos/OpenEye-python2.7-redhat-6-x64-2014.2.2/dist/OpenEye_python2.7_redhat_6_x64-2014.2.2-py2.7.egg

Alternatively you can use the /nfs/soft/python/envs/complete/latest environment. It has openeye installed.

[[Category:Internal]]